If the folders in the Projects tree are virtual folders, then they are not automatically sorted alphabetically. Right clicking on a virtual folder in Projects toolbar, you can use Move Up or Move Down to order them how you like. Depending on how the folders were added to the project file, then they may have not been sorted by default. Folders added by wildcard entries are also handled a bit differently, may be sorted differently depending on if there is a mix virtual folders and folders added via wildcard.
How were files/folders added to project? If you post your vpj file I can examine it and see. Depending on how project is organized and how files were added, we may need to address sorting or maybe add a new feature to resort folders as needed.